SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis

Zhu, Bingyao; Stülke, Jörg

doi:10.1093/nar/gkx908

Cited by 224 publications

(306 citation statements)

References 16 publications

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“…Pooled barcoded library (two samples in biological triplicates) was sequenced in a single lane at Illumina HiSeq 2000 in 50 bp singleend regime at EMBL Genomics Core Facility (Heidelberg, Germany). Gene Ontology terms are according to SubtiWiki (Zhu and Stulke, 2018 Table EV7)] and total RNA was then extracted. Reads were aligned to the B. subtilis subsp.…”

Section: Rnaseq and Rt-qpcr Validationmentioning

confidence: 99%

“…The scripts used for RNAseq data processing and analysis are available from https://github.com/mpre vorovsky/krasny-torpedo. Gene Ontology terms are according to SubtiWiki (Zhu and Stulke, 2018). For Figs 1C, D, 7B, EV3, and EV4 and Appendix Figs S1 and S5, the log2(fold change) gene expression values determined by DESeq2 are shown.…”

Section: Rnaseq and Rt-qpcr Validationmentioning

confidence: 99%

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The torpedo effect inBacillus subtilis:RNase J1 resolves stalled transcription complexes

et al. 2019

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RNase J1 is the major 5 0 -to-3 0 bacterial exoribonuclease. We demonstrate that in its absence, RNA polymerases (RNAPs) are redistributed on DNA, with increased RNAP occupancy on some genes without a parallel increase in transcriptional output. This suggests that some of these RNAPs represent stalled, non-transcribing complexes. We show that RNase J1 is able to resolve these stalled RNAP complexes by a "torpedo" mechanism, whereby RNase J1 degrades the nascent RNA and causes the transcription complex to disassemble upon collision with RNAP. A heterologous enzyme, yeast Xrn1 (5 0 -to-3 0 exonuclease), is less efficient than RNase J1 in resolving stalled Bacillus subtilis RNAP, suggesting that the effect is RNase-specific. Our results thus reveal a novel general principle, whereby an RNase can participate in genome-wide surveillance of stalled RNAP complexes, preventing potentially deleterious transcription-replication collisions.

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Section: Rnaseq and Rt-qpcr Validationmentioning

confidence: 99%

Section: Rnaseq and Rt-qpcr Validationmentioning

confidence: 99%

The torpedo effect inBacillus subtilis:RNase J1 resolves stalled transcription complexes

et al. 2019

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“…Even though B. subtilis is a well-studied organism (Zhu and Stülke, 2018), the information about the interaction between this bacterium and glyphosate as well as its potential to adapt to the herbicide is limiting. Previous studies revealed that growth of B. subtilis is inhibited by glyphosate that is due to the inhibition of the EPSP synthase (Fischer et al, 1986;Majumder et al, 1995;Selvapandiyan et al, 1995).…”

Section: Introductionmentioning

confidence: 99%

Identification of the first glyphosate transporter by genomic adaptation

Wicke

Schulz

Lentes

et al. 2019

Environmental Microbiology

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Summary The soil bacterium Bacillus subtilis can get into contact with growth‐inhibiting substances, which may be of anthropogenic origin. Glyphosate is such a substance serving as a nonselective herbicide. Glyphosate specifically inhibits the 5‐enolpyruvyl‐shikimate‐3‐phosphate (EPSP) synthase, which generates an essential precursor for de novo synthesis of aromatic amino acids in plants, fungi, bacteria and archaea. Inhibition of the EPSP synthase by glyphosate results in depletion of the cellular levels of aromatic amino acids unless the environment provides them. Here, we have assessed the potential of B. subtilis to adapt to glyphosate at the genome level. In contrast to Escherichia coli, which evolves glyphosate resistance by elevating the production and decreasing the glyphosate sensitivity of the EPSP synthase, B. subtilis primarily inactivates the gltT gene encoding the high‐affinity glutamate/aspartate symporter GltT. Further adaptation of the gltT mutants to glyphosate led to the inactivation of the gltP gene encoding the glutamate transporter GltP. Metabolome analyses confirmed that GltT is the major entryway of glyphosate into B. subtilis. GltP, the GltT homologue of E. coli also transports glyphosate into B. subtilis. Finally, we found that GltT is involved in uptake of the herbicide glufosinate, which inhibits the glutamine synthetase.

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“…The tasA coding region is located within an operon alongside two other genes: namely sipW 56 and tapA (formerly yqxM) (Zhu & Stulke, 2018). SipW is a specialised signal peptidase that is linked with 57 removal of the signal peptide from both TasA (Stover & Driks, 1999b) and TapA (Stover & Driks, 1999a) 58 during the secretion process.…”

Section: Introduction 38mentioning

confidence: 99%

The majority of the matrix protein TapA is dispensable for biofilm formation byBacillus subtilis

Earl

Arnaouteli

Sukhodub

et al. 2019

Preprint

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20 21 extracellular proteases, we show that proteolytic cleavage by these enzymes is not a prerequisite for TapA 33 function. It remains unknown why TapA is synthesized at a full length of 253 amino acids when the first 34 57 are sufficient for biofilm structuring, but the findings do not exclude the core conserved region of TapA 35 having a second role beyond that of structuring the B. subtilis biofilm. 36 37

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SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis

Cited by 224 publications

References 16 publications

The torpedo effect inBacillus subtilis:RNase J1 resolves stalled transcription complexes

The torpedo effect inBacillus subtilis:RNase J1 resolves stalled transcription complexes

Identification of the first glyphosate transporter by genomic adaptation

The majority of the matrix protein TapA is dispensable for biofilm formation byBacillus subtilis

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